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Abstract The specific role of the various pathogens causing cardiac implantable electronic devices-(CIEDs)-related infections requires further understanding. The data of 1241 patients undergoing transvenous lead extraction because of lead-related infective endocarditis (LRIE-773 patients) and pocket infection (PI-468 patients) in two high-volume centers were analyzed. Clinical course and long-term prognosis according to the pathogen were assessed. Blood and generator pocket cultures were most often positive for methicillin-sensitive Staphylococcus aureus (MSSA: 22.19% and 18.13% respectively), methicillin-sensitive Staphylococcus epidermidis (MSSE: 17.39% and 15.63%) and other staphylococci (11.59% and 6.46%). The worst long-term prognosis both in LRIE and PI subgroup was in patients with infection caused by Gram-positive microorganisms, other than staphylococci. The most common pathogens causing CIED infection are MSSA and MSSE, however, the role of other Gram-positive bacteria and Gram-negative organisms is also important. Comparable, high mortality in patients with LRIE and PI requires further studies.